make_database: Make an Reference for Gene Name Conversion

In chenyenchung/genofeatutil: Utilities for genomic feature manipulation

Description

make_database() loads gene name / ID conversion tables from online databases (e.g., FlyBase) and a user-provided GTF file that is used to annotate the features of the NGS dataset of interest (e.g., the GTF file STAR or cellranger count uses), and makes conversion tables from the loaded data.

Usage

make_database(species = "dmel", gtf.path, version = NULL)

Arguments

species	a character string describing the species of the genes. (Options: "dmel")
gtf.path	a character string containing the path to the GTF file containing the input gene names (e.g., the GTF files used by cellranger count)
version	a character specifying the version desired (e.g., "FB2019_01".)

Value

a list containing multiple coversion tables and meta data

Examples

dummypath <- system.file("extdata", "dummy.gtf",
package = "genofeatutil")
dmeldb <- make_database(species = "test",
                        gtf.path = dummypath)

chenyenchung/genofeatutil documentation built on May 15, 2019, 10:38 p.m.